Main tool: ShigaPass
Code repository: https://github.com/imanyass/ShigaPass
Additional tools:
- ncbi-blast+ 2.12.0
Basic information on how to use this tool:
###### This tool is used to predict Shigella serotypes #####
Usage : ShigaPass.sh [options]
options :
-l List of input file(s) (FASTA) with their path(s) (mandatory)
-o Output directory (mandatory)
-p Path to databases directory (mandatory)
-t Number of threads (optional, default: 2)
-u Call the makeblastdb utility for databases initialisation (optional, but required when running the script for the first time)
-k Do not remove subdirectories (optional)
-v Display the version and exit
-h Display this help and exit
Example: ShigaPass.sh -l list_of_fasta.txt -o ShigaPass_Results -p ShigaPass/ShigaPass_DataBases -t 4 -u -k
Please note that the -u option should be used when running the script for the first time and after databases updates
ShigaPass is a new in silico tool used to predict Shigella serotypes and to differentiate between Shigella, EIEC (Enteroinvasive E. coli), and non Shigella/EIEC using assembled whole genomes.
Additional information:
Full documentation: https://github.com/imanyass/ShigaPass
Included Database: Found at /ShigaPass-${version}/SCRIPT/ShigaPass_DataBases/ so for v1.5.0 use -p /ShigaPass-1.5.0/SCRIPT/ShigaPass_DataBases/. This database has already been indexed so there is no need to pass -u with your command. If you do a permissions error will occur.
ShigaPass.sh -l ShigaPass_test.txt -o ShigaPass_Results -p /ShigaPass-1.5.0/SCRIPT/ShigaPass_DataBases/